It is debatable whether if the Uganda Martyrs had not been killed in 1886, this school would have been founded. But what is not disputable is the fact that the martyrdom guided the founders, 81 years later, on the name Uganda Martyrs' S.S Namugongo. With Fifty years down the road (Golden Jubilee), and growing stronger; the inspiration of the martyrs had been indelible so much that they are extolled in the School Anthem and are implored daily to intercede for and bestow blessings on the school community. The school was founded by Late Msgr. Lawrence Mbwega, the parish priest then, who wrote a book in which he stated that three people should never be forgotten when naming founders of Uganda Martyrs' S.S Namugongo: Jeremiah Munyigwa(deceased), Hellen Namazzi and Joseph Mugerwa. The trio rallied the parents of Namugongo Catholic Parish and in 1967 they started a humble project.
Msgr. Mbwega's role was equally pivotal and together with Fr.Semwogerere guided and supported the infant institution. Joseph Nkalubo, Late Joseph Nyungwe, The Late Cosmas Lwanga, Matayo Kamya, Paul Ssemtamu, Elia Lwandasa, Leo Kibuuka, Bruno Serunkuuma and Cosmas Lwanga were also supportive in founding and budding years. On September 3 ,1967 a founders' meeting raised Ug. Shs 2,570 as start up Capital. Mbwega explains that the protectorate government did not want the multiplication of secondary Schools. Starting a secondary School was an opposition on part of the government.
"When we applied for a junior school, we were told we had to send the students to either St.Peter's Nsambya or St.Joseph's Naggalama, the only Catholic schools for the Mary Hill Fathers at the time. The children had to walk to Nsambya which was very difficult particularly for the girls. Hence the parents decided to start their own, Namugongo,"Mbwega recalls. It hence started as a community project. Mugerwa, in his nineties, attributes the driving force behind the founding of the school to Mbegwa, God-given gift of love for Children and being among them.
The School opened on January 15,1968 with 27 students and four teachers.Others were part timers from Nabisunsa Girls School and Kyambogo College School. Charles Martins was the pioneer Headmaster. Mugerwa narrates that while the target was to enroll children in the first years were from distant places."The residents were not so keen about enrolling their children at Namugongo.In the the first years the school was as local as were its students.Obwana bwali local-local !!!," he explained.